Package index
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allocateCells()
- Annotate all cells with contour level of cell type-specific density.
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cellsInRegion()
- Check which cells are in which regions
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computeDensity()
- Perform kernel density estimation on SpatialExperiment
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computeDensityHex()
- Perform kernel density estimation on SpatialExperiment
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contour2sf()
- Draw a contour region on some density level
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corDensity()
- Test for density correlation between two cell types.
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findROI()
- Find ROIs based on cell type-specific densities via graph-based method.
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getContour()
- Get contour from density
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getContourRegions()
- Calculate areas between every two density levels
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grid2sf()
- Convert x,y nodes to sf polygons
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gridDensity()
- Perform kernel density estimation on SpatialExperiment for cell types of interest
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gridSPE()
- Summarize a SpatialExperiment object at grid-level
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mergeROI()
- Manually merge ROIs
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plotCellCompo()
- Plot cell type composition in each density level of cell of interest.
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plotContour()
- Plot contour lines.
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plotContourRegion()
- Visualising an sf object (for internal use only at the moment)
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plotCorHeatmap()
- Plot model statistics using heatmap.
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plotDensCor()
- Plot density correlation between two cell types
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plotDensity()
- Plot grid-based density.
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plotGrid()
- Plot grid from metadata.
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plotROI()
- Plot ROIs on spatial.
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plotSpatial()
- Plot cells based on spatial coordinates.
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postSelRegion()
- Merge sel_region from the selectRegion function to SpatialExperiment.
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selectRegion()
- Select region of interest from plot
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spe2PB()
- Given a 'SpatialExperiment' data object, create pseudo-bulk samples using the colData information and return a DGEList object
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`[`(<SpatialExperiment>,<ANY>,<ANY>,<ANY>)
- Subset for grid level analysis